some commments and ideas on the empire tree:
what I would really like to see is something, so that I dont have to hold crtl and select every single ship (class) separately, but rather along the lines of the windows explorer's shift function. click on the first item, hold shift, click on the last item, everything inbetween including the two items are now selected. that is particularly useful when you have a lot of ships of one type, say cobalts, and you dont want all of them attack one target but rather split them up.
next, I would acutally like the double click option whereby all units of the same type are selected. with the right options there are stacked slots in the empire tree, but I am just so used to this way and maybe some others are as well, so ...
imo the current layout indicating selected units is not really clear enough, it should less transparent.
also, if you select icon stack, it would be a nice option to unstack them just the way you can with planets and stars. that way you can keep an oversight, but if you want to, you can instantly take a closer look and give more precise orders if you so desire. speaking of icon stacking, is there a rule when a new stack begins? sometimes I (or other players) have a stack of 10 and another stack f 7, sometimes I think I saw one big stack for the same amount of units. its a bit confusing.
lastly, a tough one: I love to send my fleets and units around using said empire tree, but most of the time I have to resort to the graphical representation just because I cannot remember the names am not sure if I am sending them to the right arctic world or whatever. I first thought displaying somehow the structure and phase lines of planets to one another in the empire tree would help but that makes things probably just too complicated. now, another thought might be to indicate how many jumps the voyage would be from the current position of the ships when you have a ship selection and hover over a planet. with that extra information it should be clear most of the time.